Fixing these issues first of all^^
also...
Give her a crawl...she crouches as normal, but transforms into her Morph Ball to crawl, she can lay bombs as she goes, this would allow her move in a lot better and lay traps more efficiently, I feel she would have the fastest crawl in teh game so it would allow to get out of tight situations a lot easier (and give her a better roll to boot) also hold B to charge the Bomb into a potent Power Bomb which can kill would probably have as much knockback as her fully charged shot, but requires some time to charge...
Better Fastfall speed, she gets juggled way too easily, her floatiness is one of her biggest downfalls (ironically), allowing her to get back to ground faster can greatly improve her aerial mobility and help avoid getting juggled...
Better Jabs, at least make her second hit come out faster so most characters can't get out of it so easily, especially since fast characters already have an advantage with their speed, Samus needs better options up close in general, the same with her ftilt which is pretty useless if not sweetspotted...
Rapid Firing Neutral B, In every Metroid game Samus is constantly shooting enemies with her Arm Cannon, it is her main weapon for offense, In Metroid Prime the faster you mash the faster she fires...Megaman has his lemons as his Jabs, ftilt AND his nair on a moveset that already is stocked with porjectiles, Samus can at least have a fast rapid fire on her uncharged Neutral B...When charged she can't fire them rapidly which balances it out as she can't have both rapid fire or power at the same time...
Improving her Screw Attack slightly, now I'm not saying make it so she can literally screw attack across the entire stage like she does in-game, but perhaps mashing can give her one or two extra boosts with the screw attack to mimic her in-game usage slightly better, after she uses her extra boosts she will then go into freefall...It still has the same potency at the peak of her attack...
Super Armour...How does a tiny boxer who wears a wife beater and a sweat shirt get super armour, but an armoured Suit built to withstand extreme temperatures, explosions, and heavy impacts doesn't? If she had super armour properties similar to that of Bowser where sometimes weak hits doesn't make her flinch at all then we can see Samus as a threat rather than a slow and awkward punching bag...Give her super armour on her fully Charge Neutral B, Smash attacks, Screw Attack, her currently non-existant Power Bomb and perhaps her nair and dair (initial frames)...
These changes not only make her a more viable character but also stays true to her canonical appearances as well...She's supposed to be a very versatile character within her games afterall...